visualization in chemistry - cineca...molecular obital homo/lumo: examples chemistry central journal...
TRANSCRIPT
Visualization in Chemistry
Giovanni Morelli
What is Chemistry ?
If we provide a good answer to this question
maybe we can understand what graphics
can do for chemistry … and chemists
What is Chemistry ?A possible answer
Structure
of matter
Properties
of matter
ChemistryIs one of the possibilities to
understand this link
boiling point, electrical
conductivity, specific heat,
reactivity, color….
Molecular geometry, Electron
Density, Electrostatic
Potential , Molecular orbital,…
Jmol moduleTopics covered
Introduction to basic nomenclature of the Molecular Modelling
Explanation of “some” chemical concept (we need a common vocabulary)
Discussion of some examples of “chemistry by image”
Introduction of a specific tool for the molecular visualization : Jmol
Exploring chemical proprierty on real molecules by Jmol
Today
Thursday
Molecular geometry
Electron Density
Electrostatic Potential
Molecular orbital,…
By….
Molecular Modelling
Molecular modelling encompasses all methods, theoretical and
computational, used to model or mimic the behaviour of molecules.
The action of Ritonavir, a drug against HIV. Adapting within the protease (band structure), an enzyme essential for the
spread of HIV, the Ritonavir (ball and stick) prevents the enzyme to perform its normal function in HIV propagation.
From Wikipidia
Three-dimensional structures
Stick Models Ball and Stick
Space Filling
Shows three-dimensional arrangement of atoms and bonds.
Identification of atoms requires a key of color
representations.
Shows three-dimensional arrangement as well as size
relationships between atoms.
Bonding between atoms can sometimes be difficult to
distinguish.
Focus on the geometrical structure
Three-dimensional structures
Ribbon Models
Three-dimensional Surface
A ) Van der Waals surface
B) Solvent accessible Surface ( r=1.4 Angstrom)
Molecular GeometryCoordinate system
O 0.0 0.0 0.0
C 0.0 0.0 -1.213013
H 0.0 0.937662 -1.797273
H 0.0 -0.937662 -1.797273
0 1
C1
O2 1 r2
H3 1 r3 2 a3
H4 1 r4 2 a4 3 d4
r2=1.20
r3=1.0
r4=1.0
a3=120.
a4=120.
d4=180.
y
z
21
3
4
Cartesian
Internal
3N
3N - 6
Electron Density(Electrostatic Potential)
2
i
N
1i
|)(|)ρ( rr
Source: Chlorine oxoacids pKa values from J. R. Bowser, Inorganic Chemistry (Pacific Grove, CA: Brooks-Cole,1993).
nuclei
A A
Anuclei
ZV
||)(
Rrr
| |
'd )ρ()(
rr'
rrrelettroniV
atomi
i i
iqV
||)(
Rrr
Formal charge on i-atom
Electron Density(structure/properties)
The Relationship between Delocalization of the Negative Charge in the
Oxoanions of Chlorine and the Number of Terminal Oxygen Atoms
https://saylordotorg.github.io/text_general-chemistry-principles-patterns-and-
applications-v1.0/s20-03-molecular-structure-and-acid-b.html
Molecular Obital
Frontier Orbitals
ELUMO-EHOMO = 20 eV !!!
Molecular ObitalHOMO/LUMO: Frontier Orbitals
Molecular ObitalHOMO/LUMO: The Nobel Lecture
Molecular ObitalHOMO/LUMO: examples
NH3 HOMO
Lewis base
nucleophilic
BH3 LUMO
Lewis acid
electrophile
Acid/Basic reaction
Nucleophilic substitution (SN1/SN2)
Molecular ObitalHOMO/LUMO: examples
The interaction stabilizes the unshared pair of the oxygen, while
simultaneously breaking the H-Cl bond because the interaction is
with the antibonding orbital.
The interaction stabilizes the unshared pair of the oxygen,
while simultaneously breaking the CH3-Cl bond because the
interaction is with the antibonding orbital.
Molecular ObitalHOMO/LUMO: examples
Predicted reactivity from the shape of HOMO Molecular Orbital
Molecular ObitalHOMO/LUMO: examples
Chemistry Central Journal 7(1):98 · June 2013 with 111 Reads
DOI: 10.1186/1752-153X-7-98 · Source: PubMed
In order to predict reactive sites for electrophilic and nucleophilic attack in meropenem, the MEP was
also established. The different values of electrostatic potential on the surface are represented by colors.
The positive (blue) regions of MEP show electrophilic while the negative (red) areas nucleophilic
reactivity. In meropenem, the most pronounced are the negative regions, localized on the carboxylic and
carbonyl groups, that indicate possible sites for nucleophilic activity.
Molecular ObitalHOMO/LUMO: examples
The localization of charge density on the frontier molecular
orbitals demonstrates a similar localization for the lowest
unoccupied molecular orbital and the highest occupied
molecular orbital.
For both the HOMO and LUMO, the charge density was
localized on the β-lactam and pyrrolidine 4:5 bicyclic fused
rings and the carboxylic and carbonyl groups.
Since the FMOs are the main orbitals involved in reactivity,
the 4:5 bicyclic fused rings of meropenem may be proposed
as the main areas where acceptor-donor electron reactions
occur.
The low value of HOMO-LUMO gap energy for
meropenem confirms its significant susceptibility to
degradation
Chemistry Central Journal 7(1):98 · June 2013 with 111 Reads
DOI: 10.1186/1752-153X-7-98 · Source: PubMed
Molecular ObitalPhenolphthalein colors
Acid structureBasic structure
We will analyze FMO by Jmol in the Lab….